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MAINT: Update dependency specifiers#13611

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tsbinns merged 20 commits intomainfrom
spec_zero
Jan 31, 2026
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MAINT: Update dependency specifiers#13611
tsbinns merged 20 commits intomainfrom
spec_zero

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@mne-bot mne-bot commented Jan 26, 2026 •
edited by larsoner
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Created by spec_zero GitHub action.

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larsoner approved these changes Jan 26, 2026
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Good bot 🚀

But really, nice job @tsbinns ! 👏

@larsoner larsoner enabled auto-merge (squash) January 26, 2026 19:42
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larsoner commented Jan 26, 2026

Okay failure in old is legit, need to figure out how to debug it!

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larsoner commented Jan 26, 2026

Okay looking here:

  Collecting numpy>=1.21.0 (from pyvista==0.47.dev0)
    Downloading numpy-2.2.6-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB)

it looks like we have two things to fix (at least)

  1. We need to assert something somewhere that the min versions of at least a couple things (NumPy, SciPy) stay at their intended min versions. This could be a new tools/github_actions_ensure_old.py or so that could run after the tools/github_actions_install.sh step. It could read the YAML, import some libraries, and assert the expected version matches the installed mod.__version__.
  2. We need to actually fix test_extra and/or the github_actions_install.sh step/script to make sure our old versions don't get uninstalled. In particular I don't think test_extra should install a dev version of pyvista... I think that was probably a workaround we needed at some point that we can now shouldn't need.

I'll try to push some commits for this...

@larsoner larsoner disabled auto-merge January 26, 2026 21:48
@larsoner larsoner marked this pull request as draft January 26, 2026 21:48
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larsoner commented Jan 27, 2026

Oh... we have no code for automatically updating environment_old.yml! I'll update it manually for now but we should fix this...

@larsoner larsoner marked this pull request as ready for review January 27, 2026 02:40
@larsoner larsoner requested a review from jasmainak as a code owner January 27, 2026 02:40
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tsbinns commented Jan 27, 2026

Oh... we have no code for automatically updating environment_old.yml! I'll update it manually for now but we should fix this...

This would be addressed in #13490 when it lands, but is still a WIP

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larsoner commented Jan 27, 2026

In the meantime this should be good for review @drammock , I'll fix CIs shortly but the main ideas are in here!

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tools/dev/spec_zero_update_versions.py
)
for key in opt_dependencies:
opt_dependencies[key] = update_specifiers(opt_dependencies[key], package_releases)
pyproject_data["project"]["dependencies"] = core_dependencies
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@tsbinns the old code both updated inplace and set vars, which is unnecessary (and led to some confusion where I assumed things were not updated inplace because the vars were set). I've changed it just to operate inplace where possible.

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larsoner commented Jan 27, 2026

@tsbinns actually I think this would be a good one for you to review + merge if you're happy!

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tsbinns commented Jan 27, 2026

@larsoner Sure, I'll have a look!

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LGTM. Thanks for all the work on this @larsoner!
Also gave me some things to think about for #13490.

@tsbinns tsbinns merged commit e236b2e into main Jan 31, 2026
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@tsbinns tsbinns deleted the spec_zero branch January 31, 2026 11:58
@tsbinns tsbinns mentioned this pull request Jan 31, 2026
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larsoner added a commit to teonbrooks/mne-python that referenced this pull request Feb 4, 2026
@larsoner
Merge remote-tracking branch 'upstream/main' into cnt-overflow-fix
e7e71df 
* upstream/main:
  MAINT: Work around pandas deprecation (mne-tools#13632)
  FIX: Handle empty landmarkLabels in read_raw_snirf (mne-tools#13628)
  Implement the MEF3 support (mne-tools#13610)
  BUG: Fix bug with somato dataset paths (mne-tools#13630)
  DOC: Move mne-kit-gui (mne-tools#13629)
  fix team name for inactivity tool [ci skip] (mne-tools#13626)
  MAINT: Update dependency specifiers (mne-tools#13625)
  MAINT: Update dependency specifiers (mne-tools#13611)
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@larsoner larsoner larsoner approved these changes

@tsbinns tsbinns tsbinns approved these changes

@drammock drammock Awaiting requested review from drammock drammock is a code owner

@jasmainak jasmainak Awaiting requested review from jasmainak

@agramfort agramfort Awaiting requested review from agramfort agramfort is a code owner

@dengemann dengemann Awaiting requested review from dengemann

@rob-luke rob-luke Awaiting requested review from rob-luke

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